Research workbench
Structural basis for the product specificity of histone lysine methyltransferases
Analyse Structural basis for the product specificity of histone lysine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PEG
- Type
- protein
- Length
- 534 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3 methyltransferase dim-5; Histone H3
- EC
- 2.1.1.43
- UniProt
- Q8X225, P02303
- Ligands
- SAH, ZN
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 methyltransferase dim-5 (EC 2.1.1.43) | protein | 266 | 12% helix, 22% strand | Q8X225 |
| P | Histone H3 | protein | 7 | 0% helix, 14% strand | P02303 |
| B | Histone H3 methyltransferase dim-5 (EC 2.1.1.43) | protein | 256 | 10% helix, 23% strand | Q8X225 |
| Q | Histone H3 | protein | 5 | 0% helix, 20% strand | P02303 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, P, B, Q
- ZN · Zinc ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.58 | 0.79 | 31 | SAH |
| 2 | 276 | 0.56 | 0.77 | 29 | SAH |
| 3 | 165 | 0.51 | 0.78 | 27 | empty |
| 4 | 162 | 0.47 | 0.76 | 27 | empty |
| 5 | 145 | 0.44 | 0.75 | 31 | ZN |
Interfaces
3 interfaces between chains.
- A–P · 580 Ų buried · 8 hydrogen bonds · protein-protein
- B–Q · 552 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 496 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1PEG · Structural basis for the product specificity of histone lysine methyltransferases · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X225 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase, H3 lysine-9… · a predicted model of the same protein · chain B against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8X225
- Every structure of UniProt P02303
- Elsewhere: RCSB PDB 1PEG · PDBe 1PEG · UniProt Q8X225 · UniProt P02303
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